Super-resolution (SR) is crucial for enhancing the spatial fidelity of Earth System Model (ESM) outputs, allowing fine-scale structures vital to climate science to be recovered from coarse simulations. However, traditional deep super-resolution methods, including convolutional and transformer-based models, tend to exhibit spectral bias, reconstructing low-frequency content more readily than valuable high-frequency details. In this work, we introduce two frequency-aware frameworks: the Vision Transformer-Tuned Sinusoidal Implicit Representation (ViSIR), combining Vision Transformers and sinusoidal activations to mitigate spectral bias, and the Vision Transformer Fourier Representation Network (ViFOR), which integrates explicit Fourier-based filtering for independent low- and high-frequency learning. Evaluated on the E3SM-HR Earth system dataset across surface temperature, shortwave, and longwave fluxes, these models outperform leading CNN, GAN, and vanilla transformer baselines, with ViFOR demonstrating up to 2.6~dB improvements in PSNR and significantly higher SSIM. Detailed ablation and scaling studies highlight the benefit of full-field training, the impact of frequency hyperparameters, and the potential for generalization. The results establish ViFOR as a state-of-the-art, scalable solution for climate data downscaling. Future extensions will address temporal super-resolution, multimodal climate variables, automated parameter selection, and integration of physical conservation constraints to broaden scientific applicability.

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